Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttttcgaaattgtgctattttgaatggagctaagtccggtggggttgcatgttagacaagggcctttttatgggaacagtaggattgtcctac...

Basic information

species Oryza sativa
transcript LOC_Os02g39300.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39300.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G028096_T03 (Zea mays), 5'ss of exon 11
TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttttcgaaat-tgtgctattttgaatggagctaagt--------ccggtggggttgcat--gttagacaagggcctttttatgggaacagtaggattgtcctac-------------------------------
|||||| || |||||||||||||||||||||||||||||||||||||||||||| ||||||||||  || || |||||||||||  | ||||   ||   |||| | || |||||| | || | |              | | |  ||  |||  |  |  || |  || |    |  ||  || ||| | |                                
TGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgtttttgtaaaccatgtgatcttctgaatgaaacttactggatttcttttacagagcttgatcagttttatcactgcttggttgtttttat-gtgagagtgtgccatgatcttgtttctgttccttttgtatgtacag

upper sequence: LOC_Os02g39300.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 10
TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttttcgaaattgtgct--attttgaatggagctaagtccggtggggttgcatgttagacaagggcctttttatgggaacagtaggattgtcctac----
||| || ||||| || |||||||||||||| ||||||||| | || ||||||| ||| |||||||||||| ||||||| || || ||   | |  ||    |     || |||  || |  ||   ||  |  | ||  ||||| |    ||  | ||  |||  |    | | ||| || ||     
TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatctttaatgcatttctgatcttgtgtgtactta---ccattttgatttgatgtttgttctgg--cattgaatgtaagtcattgcatt-tcttatctat

upper sequence: LOC_Os02g39300.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 5'ss of exon 10
TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttttcgaaattgtgctattttgaatggagctaagtccggtggggttgcatgttagacaagggcctttttatgggaacagtaggattgtcctac
||| || || || || ||||||||||||||||| |||||  ||||||| |||||||| || || || ||  | || || ||||| |  |       |||  | ||| |  || |     |   ||   ||   | |  |||      |    || | | |     |   ||           
TGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAGgtaatatacagtagaatctttctagt--gattttccttttctctcttgatatagactgtatagttatattctctctgtct--tcttcag-----------

upper sequence: LOC_Os02g39300.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 5'ss of exon 10
TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttttcgaaattgtgctatttt--gaatggagctaagtcc-ggtggggttgcatgttagacaagggcctttttatgggaacagtaggattgtcctac
|||||| || || ||||||||||||||||| || |||||| |||| |||||||  || ||||| ||| |  | || || ||||| || |   |     | ||| |  | |  ||    |  || ||   ||| |    |   |||  |        ||   ||  | |||  | |  |    |  
TGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAGgtaagatgaattattttcgtgatcatataggagctcatttatgttttggttgtcccgtgggttctatttca-tattggcattagtacaaaaaggataattt--

upper sequence: LOC_Os02g39300.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S402_41V6.1 (Physcomitrella patens), 5'ss of exon 10
TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgagg---tttttcgaaattgtgctattttgaatggagctaagtccggtggggt-tgcatgttagacaagggc-ctttttatgggaacagtaggattgtcctac
|||||| || ||||| || |||||||||||||| || ||| |||||||||||| ||| ||||||||| |    ||  ||| |||  |    | |||| |  ||     ||||||  |  |   |||   |||   |   |  | ||        |  |     || |||| |      | ||     
TGACCGTCGCTTGGCGGACCATTTTGGAGGGAAGCTGCATTTGGGTTATATGCAGATTCGTGAGAAGCTCGTTGACTTGCGGgtacgcgcttatttctactttccaagattttgttttcaa--aagcatggtaaagcgcgtgtattgcctggtagtgccacaaataggaatatctaagtggtgg---

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|10931057|gb|AU161331.1|AU161331
EST:     ACTTCATATGGGTTATATGCTTGATACGTGAGAAGTTATCCGAACTGCAG                         GAAGAGAAAANCAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
genomic: ACTTCATATGGGTTATATGC-TGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttt ... atgtgtacagGAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
EST: gi|29632666|gb|CB637675.1|CB637675
EST:     ATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAG                         GAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
genomic: ATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttt ... atgtgtacagGAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
EST: gi|29666474|gb|CB662749.1|CB662749
EST:     AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAG                         GAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
genomic: AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttt ... atgtgtacagGAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
EST: gi|29673663|gb|CB669938.1|CB669938
EST:     AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAG                         GAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
genomic: AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttt ... atgtgtacagGAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
EST: gi|29666475|gb|CB662750.1|CB662750
EST:     AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAG                         GAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
genomic: AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttt ... atgtgtacagGAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
EST: gi|86601880|gb|CI258556.1|CI258556
EST:     AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAG                         GAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
genomic: AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttt ... atgtgtacagGAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
EST: gi|58608959|gb|CK036992.1|CK036992
EST:     AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAG                         GAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
genomic: AACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttt ... atgtgtacagGAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
EST: gi|218503772|gb|FG969027.1|FG969027
EST:     CCGAACTGCAG                         GAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG
genomic: CCGAACTGCAGgtgaggtttt ... atgtgtacagGAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 50 (downstream exon)
Score: 22

TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttt ... atgtgtacagGAAGAGAAAAACAAAAGGCGCAAGATAGACCGAGCTGAGCATGAGAGAAG




<











<


<









Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttttcgaaattgtgctattttgaatggagctaagtccggtggggttgcatgttagacaagggcctttttatgggaacagtaggattgtcctac

- - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgggg